Molecular epidemiology and genomics of group A Streptococcus

Abstract

Streptococcus pyogenes (group A streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed.

Tissue tropisms in group A Streptococcus

“…Around that same time, three major emm pattern groups were defined based on sequence differences in the more highly conserved 3′ end of emm and flanking emm-like genes (i.e., mrp and enn ), encoding the cell wall-spanning domain of M and M-like proteins (Fig. 1a) [7–9,10▪]. emm type is highly predictive of emm pattern group based on the vast majority (97%) of GAS strains measured for both features [13] and thus, reasonably good inferences can be made for emm pattern based solely on knowledge of emm type.…”

“…The emm pattern group – known as emm patterns A–C, D, and E – displays highly significant associations with pharyngitis and impetigo [10▪,13,14]. A meta-analysis of 23 pharyngitis and six impetigo population-based surveys conducted throughout the world [10▪,11] shows that pattern A–C strains represent ~47% of pharyngitis isolates but only 8% of impetigo isolates (Fig.…”

“…A meta-analysis of 23 pharyngitis and six impetigo population-based surveys conducted throughout the world [10▪,11] shows that pattern A–C strains represent ~47% of pharyngitis isolates but only 8% of impetigo isolates (Fig. 1b); emm pattern A–C strains represent the classical throat strains and are designated ‘throat specialists’.…”

“…The emm cluster typing scheme can be applied to the emm typing and emm pattern data for the 29 population-based surveillance studies on GAS pharyngitis and impetigo infections, as reported in [10▪,11]. Figure 1c shows that more than 99% of emm pattern A–C isolates (so-called throat specialists) have an emm type belonging to clade Y, largely within clusters AC1–5.…”

Novel genomic rearrangements mediated by multiple genetic elements in Streptococcus pyogenes M23ND confer potential for evolutionary persistence

“…It is well documented that a homologous recombination of inter-and intra-strain phage genomes plays key roles in genetic diversification of phages (Hatfull, 2008), through which highly mosaic structures are formed across phage genomes (Banks et al, 2004;Bessen et al, 2015;Green et al, 2005;. The sites of homologous recombination between phages are usually located in regions of homology, such as the holin (Nakagawa et al, 2003) and the tail fibre genes (Canchaya et al, 2002).…”